Ricardo Guerreiro

Results 18 comments of Ricardo Guerreiro

Ingest won't integrate datasets of different lengths

Any update? I have the same issue with scanpy==1.8.1 The tutorial data has different row lengths and it works, so that can't be the problem

Ingest won't integrate datasets of different lengths

To try to understand what's going on, I'm sharing here a comparison of the inputs being provided to the ingest function: In the Tutorial, this is adata_ref:   | n_genes |...

Ingest won't integrate datasets of different lengths

This is the origin of the error: Some of the cells don't have neighbours at the variable adata_ref.obsp['distances'].tolil().rows: ``` array([list([223, 280, 316, 5791]), list([3877, 5899, 7766, 7807]), list([165, 304, 423,...

Ingest won't integrate datasets of different lengths

Ok, I identified the root cause of the neighbor error and reported it as a bug: https://github.com/scverse/scanpy/issues/2244 This probably happens because you have duplicated rows or cells with almost identical...

terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 1047464) > this->size() (which is 0) Aborted

What is your N50? Is it possible that very big scaffolds as input create problems?

Where have all the buscos gone?

Hey, I have the same problem. I have 90 missing Buscos in relation to QUERY (10x assembly) and 130 in relation to REFERENCE (canu assembly). Switching reference and query doesn't...

Where have all the buscos gone?

Hey, thank you both for the useful answers! @mahulchak , I used all default parameters. Here is the mummerplot of the quickmerge run: ![mumuumum](https://user-images.githubusercontent.com/25958099/62375418-8c6c0500-b53e-11e9-98ee-e523d9fb5e5f.png) So, I understand that a 10x...

nQuire not found

You should call it with a full path or export that path to the $PATH variable. So in this case you would have needed to do: ``` ./nQuire create ```...